convert_to_biostrings: Function to convert output of regulondb queries to Biostrings...

In regutools: regutools: an R package for data extraction from RegulonDB

Description

This function converts, when possible, a regulon_result object into a Biostrings object.

Usage

convert_to_biostrings(regulondb_result, seq_type = "DNA")

Arguments

regulondb_result	A regulon_result object.
seq_type	A character string with either DNA or protein, specyfing what

Value

A XStringSet object.

Author(s)

Alejandro Reyes

Examples

## Connect to the RegulonDB database if necessary
if (!exists("regulondb_conn")) regulondb_conn <- connect_database()

## Build the regulon db object
e_coli_regulondb <-
    regulondb(
        database_conn = regulondb_conn,
        organism = "E.coli",
        database_version = "1",
        genome_version = "1"
    )

## Obtain all the information from the "GENE" dataset
convert_to_biostrings(get_dataset(e_coli_regulondb, dataset = "GENE"))

regutools documentation built on Dec. 20, 2020, 2 a.m.